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Muhammad Khalid Khan Niazi PhD

TitleAssistant Professor
InstitutionWake Forest School of Medicine
DepartmentInternal Medicine, General Internal Medicine
Address
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    Collapse Biography 
    Collapse education and training
    The Ohio State University, Columbus, OhioPost Doc12/2015Imaging Informatics
    Uppsala University, Uppsala, SwedenPhD10/2011Medical Image Analysis
    Collapse awards and honors
    2023Research Excellence Award, Wake Forest University School of Medicine
    2022Early Career Investigator Award, Wake Forest University School of Medicine
    2022Research Excellence Award, Wake Forest School of Medicine
    2021 - 2023Trailblazer Award, NIBIB, NIH
    2019Research Excellence Award, Wake Forest School of Medicine
    2019Travel award, Informatics Colloquium, Wake Forest School of Medicine
    2018Best Poster award, American Urology Association: Annual Meeting, San Francisco, USA
    2018Travel award , Informatics Colloquium, Wake Forest School of Medicine
    2011Best poster award, 38th Annual Conf. of the European Teratology Society, Barcelona, Spain
    2008Best paper award, Springer: Lecture Notes in Artificial Intelligence, Leipzig, Germany

    Collapse Overview 

    Collapse Research 
    Collapse research activities and funding
         (Scott Segal)Jan 1, 2020 - Dec 31, 2021
    Anesthesia Patient Safety Foundation
    Development of machine learning algorithms to predict difficult airway management
    Role: Co-Investigator
         (Wendy L Frankel)Jan 10, 2020
    Cancer Therapy Evaluation Program (CTEP), NCI
    Computer-Assisted Analysis of Tumor Budding and Recurrence in Stage III Colon Cancer Using C89803.
    Role: Co-Investigator
         (MKK Niazi)Feb 1, 2020 - May 31, 2021
    Center for Engineering Complex Tissues Award
    Towards an Automated Image Analysis Pipeline to Compute Bioink Printability
    Role: PI
         (MKK Niazi)Mar 1, 2020 - Jun 30, 2021
    CBMI, Wake Forest School of Medicine
    A Deep Learning Approach to Measure the Histological Similarity Between Real and Regenerated Tissue Sections
    Role: PI
         (Jamie Justice)Jul 1, 2020 - Jun 30, 2021
    CTSI
    Integrating novel imaging analytics to quantify senescent cell burden in human aging and obesity
    Role: Co-PI
    1R21EB029493-01     (MKK Niazi)Apr 1, 2021 - Dec 31, 2023
    NIBIB Trailblazer Award, NIH
    Development of quantitative tools to predict patients with difficult intubation to minimize treatment related complications
    Role: PI
    CTSI Pilot Award     (Segal-Niazi)Jul 1, 2021 - Jun 30, 2022
    CTSI/NCTI/WFBMI
    Improving the Diagnosis of Obstructive Sleep Apnea Through Deep Learning.
    Role: PI
    Alliance Foundation     (Wendy L Frankel, Khalid Niazi)Jul 1, 2021 - Jun 30, 2023
    Alliance for Clinical Trials in Oncology
    Automatic detection of tumor buds in colorectal cancer patients from H&E images
    Role: Co-PI
    R21 CA273665     (Metin Gurcan)Apr 3, 2023 - Mar 31, 2025
    NIH/NCI
    Efficient and cost-effective breast cancer risk stratification using whole slide histopathology images
    Role: Co-Investigator
    R01DC020715     (Gurcan, Moberly)May 5, 2023 - Apr 30, 2028
    NIH/Department of Health and Human Services
    Computer-assisted diagnosis of ear pathologies by combining digital otoscopy with complementary data using machine learning
    Role: Co-Investigator
    1R01CA276301-01     (Khalid Niazi, Wei Chen)Jul 1, 2023 - Jun 30, 2028
    NIH/ National Cancer Institute
    An ensemble deep learning model for tumor bud detection and risk stratification in colorectal carcinoma.
    Role: Principal Investigator

    Collapse Bibliographic 
    Collapse selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
    Newest   |   Oldest   |   Most Cited   |   Most Discussed   |   Timeline   |   Field Summary   |   Plain Text
    PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Tavolara TE, Niazi MKK, Feldman AL, Jaye DL, Flowers C, Cooper LAD, Gurcan MN. Translating prognostic quantification of c-MYC and BCL2 from tissue microarrays to whole slide images in diffuse large B-cell lymphoma using deep learning. Diagn Pathol. 2024 Jan 19; 19(1):17. PMID: 38243330.
      Citations:    
    2. Su Z, Rezapour M, Sajjad U, Gurcan MN, Niazi MKK. Attention2Minority: A salient instance inference-based multiple instance learning for classifying small lesions in whole slide images. Comput Biol Med. 2023 Dec; 167:107607. PMID: 37890421.
      Citations:    
    3. Tavolara TE, Su Z, Gurcan MN, Niazi MKK. One label is all you need: Interpretable AI-enhanced histopathology for oncology. Semin Cancer Biol. 2023 Dec; 97:70-85. PMID: 37832751.
      Citations:    
    4. Gillispie GJ, Copus J, Uzun-Per M, Yoo JJ, Atala A, Niazi MKK, Lee SJ. The correlation between rheological properties and extrusion-based printability in bioink artifact quantification. Mater Des. 2023 Sep; 233. PMID: 37854951.
      Citations:    
    5. Bunch PM, Rigdon J, Niazi MKK, Barnard RT, Boutin RD, Houston DK, Lenchik L. Association of CT-Derived Skeletal Muscle and Adipose Tissue Metrics with Frailty in Older Adults. Acad Radiol. 2023 Jul 19. PMID: 37479618.
      Citations:    
    6. Sajjad U, Rezapour M, Su Z, Tozbikian GH, Gurcan MN, Niazi MKK. NRK-ABMIL: Subtle Metastatic Deposits Detection for Predicting Lymph Node Metastasis in Breast Cancer Whole-Slide Images. Cancers (Basel). 2023 Jun 30; 15(13). PMID: 37444538.
      Citations:    
    7. Rezapour M, Niazi MKK, Gurcan MN. Author Correction: Machine learning-based analytics of the impact of the Covid-19 pandemic on alcohol consumption habit changes among United States healthcare workers. Sci Rep. 2023 Apr 26; 13(1):6818. PMID: 37100854.
      Citations:    
    8. Rezapour M, Niazi MKK, Gurcan MN. Machine learning-based analytics of the impact of the Covid-19 pandemic on alcohol consumption habit changes among United States healthcare workers. Sci Rep. 2023 Apr 12; 13(1):6003. PMID: 37046069.
      Citations:    
    9. Su Z, Niazi MKK, Tavolara TE, Niu S, Tozbikian GH, Wesolowski R, Gurcan MN. BCR-Net: A deep learning framework to predict breast cancer recurrence from histopathology images. PLoS One. 2023; 18(4):e0283562. PMID: 37014891.
      Citations:    
    10. Moaven O, Tavolara TE, Valenzuela CD, Cheung TT, Corvera CU, Cha CH, Stauffer JA, Niazi MKK, Gurcan MN, Shen P. Machine Learning Models for Predicting the Outcomes of Surgical Treatment of Colorectal Liver Metastases. J Am Coll Surg. 2023 Apr 01; 236(4):884-893. PMID: 36727981.
      Citations:    
    11. Tavolara TE, Gurcan MN, Niazi MKK. Contrastive Multiple Instance Learning: An Unsupervised Framework for Learning Slide-Level Representations of Whole Slide Histopathology Images without Labels. Cancers (Basel). 2022 Nov 24; 14(23). PMID: 36497258.
      Citations:    
    12. Su Z, Tavolara TE, Carreno-Galeano G, Lee SJ, Gurcan MN, Niazi MKK. Attention2majority: Weak multiple instance learning for regenerative kidney grading on whole slide images. Med Image Anal. 2022 Jul; 79:102462. PMID: 35512532.
      Citations:    
    13. Luchini C, Pantanowitz L, Adsay V, Asa SL, Antonini P, Girolami I, Veronese N, Nottegar A, Cingarlini S, Landoni L, Brosens LA, Verschuur AV, Mattiolo P, Pea A, Mafficini A, Milella M, Niazi MK, Gurcan MN, Eccher A, Cree IA, Scarpa A. Ki-67 assessment of pancreatic neuroendocrine neoplasms: Systematic review and meta-analysis of manual vs. digital pathology scoring. Mod Pathol. 2022 Mar 05. PMID: 35249100.
      Citations:    
    14. Koyuncu D, Niazi MKK, Tavolara T, Abeijon C, Ginese ML, Liao Y, Mark C, Specht A, Gower AC, Restrepo BI, Gatti DM, Kramnik I, Gurcan M, Yener B, Beamer G. CXCL1: A new diagnostic biomarker for human tuberculosis discovered using Diversity Outbred mice. PLoS Pathog. 2021 Aug 17; 17(8):e1009773. PMID: 34403447.
      Citations:    
    15. Tavolara TE, Gurcan MN, Segal S, Niazi MKK. Identification of difficult to intubate patients from frontal face images using an ensemble of deep learning models. Comput Biol Med. 2021 Aug 04; 136:104737. PMID: 34391000.
      Citations:    
    16. Tavolara TE, Niazi MKK, Gower AC, Ginese M, Beamer G, Gurcan MN. Deep learning predicts gene expression as an intermediate data modality to identify susceptibility patterns in Mycobacterium tuberculosis infected Diversity Outbred mice. EBioMedicine. 2021 May; 67:103388. PMID: 34000621.
      Citations:    
    17. Meryem Uzun-Per, Gregory J Gillispie, Thomas Erol Tavolara, James J Yoo, Anthony Atala, Metin Nafi Gurcan, Sang Jin Lee, Muhammad Khalid Khan Niazi. Automated Image Analysis Methodologies to Compute Bioink Printability . Wiley, Advanced Engineering Materials. 2020. View Publication.
    18. Binol H, Niazi MKK, Essig G, Shah J, Mattingly JK, Harris MS, Elmaraghy C, Teknos T, Taj-Schaal N, Yu L, Gurcan MN, Moberly AC. Digital Otoscopy Videos Versus Composite Images: A Reader Study to Compare the Accuracy of ENT Physicians. Laryngoscope. 2021 05; 131(5):E1668-E1676. PMID: 33170529.
      Citations:    
    19. Tavolara TE, Niazi MKK, Ginese M, Piedra-Mora C, Gatti DM, Beamer G, Gurcan MN. Automatic discovery of clinically interpretable imaging biomarkers for Mycobacterium tuberculosis supersusceptibility using deep learning. EBioMedicine. 2020 Dec; 62:103094. PMID: 33166789.
      Citations:    
    20. Gillispie GJ, Han A, Uzun-Per M, Fisher J, Mikos AG, Niazi MKK, Yoo JJ, Lee SJ, Atala A. The Influence of Printing Parameters and Cell Density on Bioink Printing Outcomes. Tissue Eng Part A. 2020 Dec; 26(23-24):1349-1358. PMID: 32928068.
      Citations:    
    21. Binol H., Moberly AC, Niazi MKK, Essig G, Shah J, Elmaraghy C, Teknos T, Taj-Schaal N, Yu L, Gurcan MN. . , 10(17), p.5894. MDPI Applied Sciences. SelectStitch: automated frame segmentation and stitching to create composite images from Otoscope video clips. 2020; 10(17):5894. View Publication.
    22. Muhammad Khalid Khan Niazi, Enes Yazgan, Thomas E. Tavolara, Wencheng Li, Cheryl T. Lee, Anil Parwani, Metin N. Gurcan . Semantic segmentation to identify bladder layers from H&E Images. BMC Springer Nature Diagnostic Pathology. 2020; 15.
    23. Niazi MKK, Yazgan E, Tavolara TE, Li W, Lee CT, Parwani A, Gurcan MN. Semantic segmentation to identify bladder layers from H&E Images. Diagn Pathol. 2020 Jul 16; 15(1):87. PMID: 32677978.
      Citations:    
    24. Camalan S, Niazi MKK, Moberly AC, Teknos T, Essig G, Elmaraghy C, Taj-Schaal N, Gurcan MN. OtoMatch: Content-based eardrum image retrieval using deep learning. PLoS One. 2020; 15(5):e0232776. PMID: 32413096.
      Citations:    
    25. Tavolara TE, Niazi MKK, Arole V, Chen W, Frankel W, Gurcan MN. Author Correction: A modular cGAN classification framework: Application to colorectal tumor detection. Sci Rep. 2020 Feb 06; 10(1):2398. PMID: 32024961.
      Citations:    
    26. Binol H, Plotner A, Sopkovich J, Kaffenberger B, Niazi MKK, Gurcan MN. Ros-NET: A deep convolutional neural network for automatic identification of rosacea lesions. Skin Res Technol. 2020 May; 26(3):413-421. PMID: 31849118.
      Citations:    
    27. Tavolara TE, Niazi MKK, Arole V, Chen W, Frankel W, Gurcan MN. A modular cGAN classification framework: Application to colorectal tumor detection. Sci Rep. 2019 12 12; 9(1):18969. PMID: 31831792.
      Citations:    
    28. Niazi MKK, Parwani AV, Gurcan MN. Digital pathology and artificial intelligence. Lancet Oncol. 2019 05; 20(5):e253-e261. PMID: 31044723.
      Citations:    
    29. Senaras C, Niazi MKK, Lozanski G, Gurcan MN. DeepFocus: Detection of out-of-focus regions in whole slide digital images using deep learning. PLoS One. 2018; 13(10):e0205387. PMID: 30359393.
      Citations:    
    30. Niazi MKK, Lin Y, Liu F, Ashok A, Marcellin MW, Tozbikian G, Gurcan MN, Bilgin A. Pathological image compression for big data image analysis: Application to hotspot detection in breast cancer. Artif Intell Med. 2019 04; 95:82-87. PMID: 30266546.
      Citations:    
    31. Niazi MKK, Senaras C, Pennell M, Arole V, Tozbikian G, Gurcan MN. Relationship between the Ki67 index and its area based approximation in breast cancer. BMC Cancer. 2018 Sep 03; 18(1):867. PMID: 30176814.
      Citations:    
    32. Niazi MKK, Abas FS, Senaras C, Pennell M, Sahiner B, Chen W, Opfer J, Hasserjian R, Louissaint A, Shana'ah A, Lozanski G, Gurcan MN. Nuclear IHC enumeration: A digital phantom to evaluate the performance of automated algorithms in digital pathology. PLoS One. 2018; 13(5):e0196547. PMID: 29746503.
      Citations:    
    33. Senaras C, Niazi MKK, Sahiner B, Pennell MP, Tozbikian G, Lozanski G, Gurcan MN. Optimized generation of high-resolution phantom images using cGAN: Application to quantification of Ki67 breast cancer images. PLoS One. 2018; 13(5):e0196846. PMID: 29742125.
      Citations:    
    34. Niazi MKK, Tavolara TE, Arole V, Hartman DJ, Pantanowitz L, Gurcan MN. Identifying tumor in pancreatic neuroendocrine neoplasms from Ki67 images using transfer learning. PLoS One. 2018; 13(4):e0195621. PMID: 29649302.
      Citations:    
    35. Niazi MKK, Beamer G, Gurcan MN. An application of transfer learning to neutrophil cluster detection for tuberculosis: Efficient implementation with nonmetric multidimensional scaling and sampling. Proc SPIE Int Soc Opt Eng. 2018; 10581. PMID: 34262235.
      Citations:    
    36. Mei Y, Diemer PJ, Niazi MR, Hallani RK, Jarolimek K, Day CS, Risko C, Anthony JE, Amassian A, Jurchescu OD. Crossover from band-like to thermally activated charge transport in organic transistors due to strain-induced traps. Proc Natl Acad Sci U S A. 2017 08 15; 114(33):E6739-E6748. PMID: 28739934.
      Citations:    
    37. Arbab M, Tahir S, Niazi MK, Ishaq M, Hussain A, Siddique PM, Saeed S, Khan WA, Qamar R, Butt AM, Azam M. TNF-a Genetic Predisposition and Higher Expression of Inflammatory Pathway Components in Keratoconus. Invest Ophthalmol Vis Sci. 2017 07 01; 58(9):3481-3487. PMID: 28702675.
      Citations:    
    38. Niazi MKK, Chung JH, Heaton-Johnson KJ, Martinez D, Castellanos R, Irwin MS, Master SR, Pawel BR, Gurcan MN, Weiser DA. Advancing Clinicopathologic Diagnosis of High-risk Neuroblastoma Using Computerized Image Analysis and Proteomic Profiling. Pediatr Dev Pathol. 2017 Sep-Oct; 20(5):394-402. PMID: 28420318.
      Citations:    
    39. Abas FS, Shana'ah A, Christian B, Hasserjian R, Louissaint A, Pennell M, Sahiner B, Chen W, Niazi MKK, Lozanski G, Gurcan M. Computer-assisted quantification of CD3+ T cells in follicular lymphoma. Cytometry A. 2017 06; 91(6):609-621. PMID: 28110507.
      Citations:    
    40. Niazi MK, Chung JH, Heaton-Johnson KJ, Martinez D, Castellanos R, Irwin M, Master SR, Pawel B, Gurcan MN, Weiser D. Advancing clinicopathologic diagnosis of high-risk neuroblastoma using computerized image analysis and proteomic profiling. Pediatr Dev Pathol. 2016 Jul 21. PMID: 27442894.
      Citations:    
    41. Niazi MKK, Zynger DL, Clinton SK, Chen J, Koyuturk M, LaFramboise T, Gurcan M. Visually Meaningful Histopathological Features for Automatic Grading of Prostate Cancer. IEEE J Biomed Health Inform. 2017 07; 21(4):1027-1038. PMID: 28113734.
      Citations:    
    42. Saleem S, Azam A, Maqsood SI, Muslim I, Bashir S, Fazal N, Riaz M, Ali SH, Niazi MK, Ishaq M, Waheed NK, Qamar R, Azam M. Role of ACE and PAI-1 Polymorphisms in the Development and Progression of Diabetic Retinopathy. PLoS One. 2015; 10(12):e0144557. PMID: 26658948.
      Citations:    
    43. Niazi MK, Dhulekar N, Schmidt D, Major S, Cooper R, Abeijon C, Gatti DM, Kramnik I, Yener B, Gurcan M, Beamer G. Lung necrosis and neutrophils reflect common pathways of susceptibility to Mycobacterium tuberculosis in genetically diverse, immune-competent mice. Dis Model Mech. 2015 Sep; 8(9):1141-53. PMID: 26204894.
      Citations:    
    44. Harrison DE, Astle CM, Niazi MKK, Major S, Beamer GL. Genetically diverse mice are novel and valuable models of age-associated susceptibility to Mycobacterium tuberculosis. Immun Ageing. 2014; 11(1):24. PMID: 25606048.
      Citations:    
    45. Kornaropoulos EN, Niazi MK, Lozanski G, Gurcan MN. Histopathological image analysis for centroblasts classification through dimensionality reduction approaches. Cytometry A. 2014 Mar; 85(3):242-55. PMID: 24376080.
      Citations:    
    46. Niazi MK, Beamer G, Gurcan MN. Detecting and characterizing cellular responses to Mycobacterium tuberculosis from histology slides. Cytometry A. 2014 Feb; 85(2):151-61. PMID: 24339210.
      Citations:    
    47. Das H, Wang Z, Niazi MK, Aggarwal R, Lu J, Kanji S, Das M, Joseph M, Gurcan M, Cristini V. Impact of diffusion barriers to small cytotoxic molecules on the efficacy of immunotherapy in breast cancer. PLoS One. 2013; 8(4):e61398. PMID: 23620747.
      Citations:    
    48. Abela D, Ritchie H, Ababneh D, Gavin C, Nilsson MF, Khan MK, Carlsson K, Webster WS. The effect of drugs with ion channel-blocking activity on the early embryonic rat heart. Birth Defects Res B Dev Reprod Toxicol. 2010 Oct; 89(5):429-40. PMID: 20973055.
      Citations:    
    49. Muhammad Talal Ibrahim, M Aurangzeb Khan, Khurram Saleem Alimgeer, Muhammad Khalid Khan, Imtiaz A Taj, Ling Guan. Velocity and pressure-based partitions of horizontal and vertical trajectories for on-line signature verification. Elsevier Pattern Recognition. 2010; 43(8):2817-2832. View Publication.
    50. Nilsson MF, Danielsson C, Sköld AC, Johansson A, Blomgren B, Wilson J, Khan KM, Bengtsson E, Kultima K, Webster WS, Danielsson BR. Improved methodology for identifying the teratogenic potential in early drug development of hERG channel blocking drugs. Reprod Toxicol. 2010 Apr; 29(2):156-63. PMID: 20144703.
      Citations:    
    51. Khan MA, Niazi MK, Khan MA. Velocity-image model for online signature verification. IEEE Trans Image Process. 2006 Nov; 15(11):3540-9. PMID: 17076411.
      Citations:    
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